Whole wheat cinnamon rolls combine the nutty, hearty flavor of whole wheat flour with a rich, sweet cinnamon filling for a deliciously comforting treat. Using a delayed fermentation method, this two-day recipe allows the dough to slowly rise, resulting in rolls that are perfectly soft, airy, and full of flavor.
There’s just something magical about the smell of freshly baked cinnamon rolls, and believe it or not, they actually taste even better when made with whole wheat.
These whole wheat cinnamon rolls bring a bit of wholesome goodness to the classic treat, with the nutty flavor of whole wheat flour and a touch of honey to make the dough extra tender and sweet. The recipe takes a couple of days to make, but don’t let that scare you off—it’s mostly hands-off time, and the results are totally worth it.
I’m using Peter Reinhart’s recipe from his book, Whole Grain Breads. He has some pretty spectacular methods for transforming whole wheat into deliciously tender and flavorful breads, without the “rough” texture or flavor most people associate with whole grains.
The trick is a long, slow fermentation so that the yeast and natural enzymes in the wheat itself have plenty of time to work.
The dough uses a delayed fermentation method, which means it has time to develop a richer flavor. You’ll start by preparing two pre-doughs—one called a “soaker” and the other a “biga.” These get mixed up the day before and then left to rest overnight, so the flavors can really come together. When you’re ready to bake the rolls, you’ll mix the pre-doughs with a little extra flour, salt, yeast, and melted butter, then shape it all into rolls that get a good rise before they hit the oven.
Once baked, these rolls are soft, fluffy, and just the right amount of sweet with cinnamon sugar filling rolled up inside. And to make them even more special, you can top them with a simple glaze—either a smooth fondant glaze or a rich cream cheese and honey glaze, depending on what you’re in the mood for.
Although these rolls require a bit of planning, the process is pretty straightforward, and you’ll be rewarded with a batch of delicious cinnamon rolls that’s perfect for a cozy morning or a treat to share with family and friends.
How to Make Whole Wheat Cinnamon Rolls
Makes: 8 to 10 Cinnamon Rolls
Total Time: 2 days (but most of it is hands-off!)
Day 1: Prepare the Soaker and Biga
Soaker Ingredients:
- 1 ¾ cups (227 g) whole wheat flour
- ½ tsp (4 g) salt
- ¾ cup (170 g) milk (or buttermilk, soy milk, or rice milk)
Biga Ingredients:
- 1 ¾ cups (227 g) whole wheat flour
- 1/4 tsp (1 g) instant yeast
- ⅔ cup (160 g) Milk (or buttermilk, soy milk, or rice milk)
- 1 large egg (about 50 g), slightly beaten
Instructions for Day 1:
Start by making the soaker.
In a bowl, mix together the soaker ingredients (whole wheat flour, salt and milk). Stir everything together until it forms a dough ball.
Cover the bowl loosely with plastic wrap and let it sit at room temperature for 12 to 24 hours.
If you need to leave it longer, no worries! Just pop it in the fridge, where it will stay good for up to 3 days. When you’re ready to use it, take it out of the fridge about 2 hours before you’re ready to mix the final dough.
Next, it’s time to prepare the biga.
In a separate bowl, combine whole wheat flour, yeast, milk, and a beaten egg. Stir everything together until you’ve got a sticky dough.
Use wet hands to knead it for about 2 minutes to make sure everything is well-mixed. Let it rest for 5 minutes, then knead it again for another minute.
Once it’s all set, cover the dough tightly with plastic wrap and pop it in the fridge. It’ll need at least 8 hours to chill, but you can leave it in the fridge for up to 3 days if needed.
Day 2: Final Dough and Baking
Final Dough Ingredients:
- All of the soaker (from Day 1)
- All of the biga (from Day 1)
- 7 tbsp (55 g) whole wheat flour
- 3/4 tsp (5 g) salt
- 2 1/4 tsp (7 g) instant yeast
- 3 tbsp (60 g) honey (or agave nectar, or brown sugar)
- 1/4 cup unsalted butter, melted (or vegetable oil)
- 1/2 cup cinnamon sugar (6 1/2 tbsp sugar + 2 1/2 tbsp ground cinnamon)
- Extra flour for adjustments
- Optional: cream cheese and honey glaze
Instructions for Day 2
Alright, let’s jump into Day 2! Start by chopping up the soaker and biga into small pieces—about 12 pieces of each—using a metal pastry scraper. Toss them into a large bowl.
Add in the 7 tbsp of flour, salt, yeast, honey, and melted butter. Now, stir everything together really well with a big spoon, or use your hands to knead the dough for about 2 minutes. The dough should be soft, a little sticky, but well-mixed.
Next, transfer the dough onto a floured surface and knead it for 3 to 4 minutes. If it’s sticking, sprinkle in a little more flour, but try to keep it soft and tacky, not too dry. Once it’s all smooth, shape it into a ball and let it rest for about 5 minutes.
After that, give the dough one final knead for about a minute to strengthen the gluten. Then, form it into a ball and pop it into a lightly oiled bowl. Roll it around to coat in the oil, cover loosely with plastic wrap, and let it rise for 45 to 60 minutes. It should puff up to about 1.25 times its original size.
When the dough is ready, lightly dust your work surface with flour and roll the dough out into a 9-inch square, about 1/4-inch thick. Sprinkle the cinnamon sugar evenly over the surface, then roll it up tightly into a log. Slice it into 1-inch thick rolls and place them about 1 inch apart on a sheet pan lined with parchment paper.
Cover them loosely with plastic wrap or a towel, and let them rise at room temperature for another 45 to 60 minutes. They should nearly double in size.
While the rolls are proofing, preheat your oven to 400°F (204°C). Once the rolls have risen, pop the pan in the oven, lower the heat to 350°F (177°C), and bake for 15 minutes. After that, rotate the pan 180 degrees and bake for another 10 to 15 minutes. The rolls should be golden brown and feel springy when you press them in the center. If they still feel doughy, give them a little more time.
Once they’re done, remove them from the oven and let them cool for about 5 minutes before glazing. Enjoy the delicious smell and dig in!

Whole Wheat Cinnamon Rolls
Ingredients
For the Soaker:
- 1 ¾ cups 227 g whole wheat flour
- ½ tsp 4 g salt
- ¾ cup 170 g milk (or buttermilk, soy milk, or rice milk)
For the Biga:
- 1 ¾ cups 227 g whole wheat flour
- 1/4 tsp 1 g instant yeast
- ⅔ cup 160 g Milk (or buttermilk, soy milk, or rice milk)
- 1 large egg about 50 g, slightly beaten
For the Final Dough:
- All of the soaker from Day 1
- All of the biga from Day 1
- 7 tbsp 55 g whole wheat flour
- 3/4 tsp 5 g salt
- 2 1/4 tsp 7 g instant yeast
- 3 tbsp 60 g honey (or agave nectar, or brown sugar)
- 1/4 cup unsalted butter melted (or vegetable oil)
- 1/2 cup cinnamon sugar 6 1/2 tbsp sugar + 2 1/2 tbsp ground cinnamon
- Extra flour for adjustments
- Optional: cream cheese and honey glaze see below
Instructions
Instructions for Day 1:
- Make the Soaker: In a bowl, combine whole wheat flour, salt, and milk. Stir to form a ball of dough. Cover loosely with plastic wrap and leave it at room temperature for 12 to 24 hours. If you plan to leave it longer, refrigerate it (good for up to 3 days), removing it from the fridge 2 hours before mixing the final dough.
- Prepare the Biga: In a separate bowl, mix together whole wheat flour, yeast, milk, and egg until a sticky dough forms. Knead for 2 minutes with wet hands to distribute the ingredients evenly. Let it rest for 5 minutes, then knead again for 1 more minute. Cover the dough tightly with plastic wrap and refrigerate for 8 hours or up to 3 days.
Instructions for Day 2:
- Mix the Dough: Using a metal pastry scraper, chop the soaker and biga into smaller pieces (12 pieces each) and place them in a large bowl. Add the flour, salt, yeast, honey, and melted butter. Stir vigorously with a large spoon or knead by hand for 2 minutes, until all ingredients are evenly incorporated and the dough becomes soft and slightly sticky.
- Knead the Dough: Transfer the dough to a floured work surface and knead for 3 to 4 minutes, incorporating as much extra flour as needed. The dough should feel soft and tacky but not sticky. Shape the dough into a ball and let it rest for 5 minutes.
- Final Knead and First Rise: Knead the dough for another minute to strengthen the gluten. Form it into a ball and place it in a lightly oiled bowl, rolling it to coat in the oil. Cover loosely with plastic wrap and let rise for 45 to 60 minutes, or until the dough is about 1.25 times its original size.
- Shape the Cinnamon Rolls: Lightly dust your work surface with flour and transfer the dough to it. Roll the dough into a 9-inch square, approximately 1/4-inch thick. Sprinkle the cinnamon sugar evenly over the dough, then roll it up tightly into a log. Slice the dough into 1-inch thick rolls and place them 1 inch apart on a sheet pan lined with parchment paper.
- Proof the Rolls: Mist the tops of the rolls with pan spray, cover loosely with plastic wrap, and let rise at room temperature for 45 to 60 minutes, or until the rolls are nearly double in size.
- Preheat the Oven and Bake: Preheat your oven to 400°F (204°C). Place the pan in the oven, lower the temperature to 350°F (177°C), and bake for 15 minutes. Rotate the pan 180 degrees and continue baking for another 10 to 15 minutes. The rolls should be golden brown and springy when pressed in the center. If they still feel doughy, continue baking.
- Glaze and Serve: Once the rolls are baked, remove them from the oven and cool for 5 minutes before glazing.
Notes
- 1 cup confectioners' sugar
- 2 tbsp milk
- 1/2 tsp vanilla, lemon, orange, or almond extract (optional)
- 4 oz cream cheese
- 3 tbsp maple syrup (or honey)
- 2 tbsp milk
- 1 tsp vanilla extract
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